def analyze(self):
image_set = ImageSet(self.in_path)
image_set.sort()
report_gen = CSVReportGenerator(os.path.join(self.report_path, 'noise_analysis.csv'))
counter = 1
print 'Extracting using %s' % self.method_name
for image in sorted(image_set, key=lambda img: img.filename):
filename = os.path.splitext(os.path.basename(image.filename))[0]
noise = self.analyze_single(image)
#print 'Analyzing %d/%d: %s' % (counter, len(image_set.filelist), filename)
print '%.2f' % noise
counter += 1
report_gen.generate()
def extract(self):
image_set = ImageSet(self.data_path)
image_set.sort()
output_path = os.path.join(self.result_path,
self.__experiment.name + '.csv')
report_gen = CSVReportGenerator(output_path, params=self.params)
counter = 1
print 'Extracting using %s' % self.method_name
for image in sorted(image_set, key=lambda img: img.filename):
filename = os.path.splitext(os.path.basename(image.filename))[0]
instance = session.query(Analysis).filter_by(
filename=image.filename,
experiment_name=self.__experiment.name,
experiment_params=self.__experiment.params).first()
if instance:
analysis = instance
else:
try:
analysis = self.analyze_mono_bead(image)
analysis.experiment = self.__experiment
session.add(analysis)
print 'Analyzing %d/%d: %s' % (
counter, len(image_set.filelist), filename)
except NoBeadException:
print 'No Bead Exception: %s' % filename
# Sholl Analysis Plots
#self.plot_sholl_analysis(analysis, filename)
# Add to overall report
report_gen.add_analysis(filename, analysis)
counter += 1
session.commit()
report_gen.generate()
